1 Supplementary Figure Legends Supplementary Figure 1. Magnified image for the colony-formation assays shown in Fig. 3A. Supplementary Figure 2. The mRNA expression level of NR1I2 in endogenously NR1I2-positive cells (SK-N-KP) as well as stably transfected cells (SMS-KAN-B1, SMS-KAN-B2, and GOTO-A1) and their mock-transfected control (KAN-vector and GOTO-vector). Supplementary Figure 3. Representative results of RT-PCR analysis revealed up-regulation of CYP3A4, a known transcriptional target of NR1I2, in VP-16-NR1/2, underscoring the reliability of our system for detecting target genes. 2 Supplementary Table Up-regulated genes in NR1I2-stably expressing NB cells Ratio Acc. number Gene symbol Description Chr. Location 1st 2nd Cell cycle / Cell death /Differentiation NM 003914 1 CCNA1 cyclin A1 13q12.3-q13 1.89 1.92 NM 003503 1 CDC7L1 CDC7 cell division cycle 7-like 1 (S. cerevisiae) 1p22 1.84 1.86 NM 004208 1 PDCD8 programmed cell death 8 (apoptosis-inducing factor) Xq25-q26 2.00 2.03 NM 000465 1 BARD1 BRCA1 associated RING domain 1 2q34-q35 1.90 1.93 NM 000127 1 EXT1 exostoses (multiple) 1 8q24.11-q24.13 1.87 1.89 NM 016341 1 PLCE1 phospholipase C, epsilon 1 10q23 2.89 2.94 NM_004613_1 TGM2 transglutaminase 2 (C polypeptide, protein-glutamine-gamma- 20q12 1.59 1.62 glutamyltransferase) NM 004907 1 ETR101 immediate early protein 19p13.13 1.65 1.67 NM 003389 1 CORO2A coronin, actin binding protein, 2A 9q22.3 1.71 1.73 NM 005876 1 APEG1 aortic preferentially expressed protein 1 2q36.3 1.88 1.91 Signaling pathway NM 013324 1 CISH cytokine inducible SH2-containing protein 3p21.3 2.14 2.17 NM 000455 1 STK11 serine/threonine kinase 11 (Peutz-Jeghers syndrome) 19p13.3 1.62 1.64 NM 005167 1 ARHC ras homolog gene family, member C 1p21-p13 1.50 1.52 NM 001667 1 ARL2 ADP-ribosylation factor-like 2 11q13 1.51 1.53 NM 006189 1 OMP olfactory marker protein 11q13.5 1.55 1.58 XM 032838 1 GUCY1A3 guanylate cyclase 1, soluble, alpha 3 4q31.1-q31.2 1.60 1.63 Cell adhesion NM 031500 1 PCDHA4 protocadherin alpha 4 5q31 1.94 1.97 NM 024003 1 L1CAM L1 cell adhesion molecule Xq28 1.87 1.89 NM 018930 1 PCDHB10 protocadherin beta 10 5q31 1.63 1.66 NM 016522 1 HNT neurotrimin 11q25 1.55 1.57 NM 003259 1 ICAM5 intercellular adhesion molecule 5, telencephalin 19p13.2 1.52 1.54 Transcription-related genes NM 030380 1 GLI2 GLI-Kruppel family member GLI2 2q14 2.68 2.72 NM 002359 1 MAFG v-maf musculoaponeurotic fibrosarcoma oncogene homolog G (avian) 17q25 2.51 2.55 NM 005170 1 ASCL2 achaete-scute complex-like 2 (Drosophila) 11p15.5 2.43 2.46 NM 014553 1 LBP-9 LBP protein; likely ortholog of mouse CRTR-1 2q14 1.93 1.95 NM 018489 1 ASH1 hypothetical protein ASH1 1q21.2 1.81 1.83 NM 006756 1 TCEA1 transcription elongation factor A (SII), 1 3p22-p21.3 1.54 1.56 NM 002729 1 HHEX hematopoietically expressed homeobox 10q24.1 1.55 1.57 NM 003935 1 TOP3B topoisomerase (DNA) III beta 22q11.22 1.59 1.61 NM 015339 1 ADNP activity-dependent neuroprotector 20q13.13-q13.2 1.61 1.63 NM 004182 1 UXT ubiquitously-expressed transcript Xp11.23- 2.90 2.94 NM 003893 1 LDB1 LIM domain binding 1 10q24-q25 1.58 1.60 NM 005663 1 WHSC2 Wolf-Hirschhorn syndrome candidate 2 4p16.3 1.65 1.67 Receptor / membrane protein NM_006840_1 LILRB5 leukocyte immunoglobulin-like receptor, subfamily B (with TM and 19q13.4 1.73 1.76 ITIM domains), member 5 NM_004631_1 LRP8 low density lipoprotein receptor-related protein 8, apolipoprotein e 1p34 1.52 1.54 receptor NM_022965_1 FGFR3 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric 4p16.3 1.56 1.59 dwarfism) NM 025141 1 BLP2 BBP-like protein 2 15q26.3 1.51 1.53 NM 016447 1 MPP6 membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 7p15 1.67 1.70 NM 005727 1 TSPAN-1 tetraspan 1 1p34.1 1.67 1.69 NM_000484_1 APP amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer 21q21.3 2.03 2.05 Ion channel / transpor NM 012456 1 TIMM10 translocase of inner mitochondrial membrane 10 homolog (yeast) 11q12.1-q12.3 1.87 1.89 NM 003172 1 SURF1 surfeit 1 9q34.2 1.92 1.95 NM 006188 1 OCM oncomodulin 7p13-p11 1.7 1.72 NM 002243 1 KCNJ15 potassium inwardly-rectifying channel, subfamily J, member 15 21q22.2 1.88 1.91 NM 004588 1 SCN2B sodium channel, voltage-gated, type II, beta polypeptide 11q23 1.52 1.54 NM 021625 1 TRPV4 transient receptor potential cation channel, subfamily V, member 4 12q24.1 1.77 1.80 NM 005829 1 AP3S2 adaptor-related protein complex 3, sigma 2 subunit 15q25.2 2.51 2.55 NM 018484 1 SLC22A11 solute carrier family 22 (organic anion/cation transporter), member 11 11q13.1 1.66 1.68 NM 006224 1 PITPN phosphotidylinositol transfer protein 17p13.3 1.73 1.75 NM 005063 1 SCD stearoyl-CoA desaturase (delta-9-desaturase) 10q23-q24 1.74 1.77 NM 016176 1 Cab45 calcium binding protein Cab45 precursor 1p36.33 1.84 1.86 3 (Table. Continued) Ratio Acc. number Gene symbol Description Chr. Location 1st 2nd Homeostasis / metabolic enzymes NM 004776 1 B4GALT5 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 20q13.1-q13.2 1.54 1.56 NM 019894 1 TMPRSS4 transmembrane protease, serine 4 11q23.3 1.55 1.57 NM_021599_1 ADAMTS2 a disintegrin-like and metalloprotease (reprolysin type) with 5qter 1.58 1.60 thrombospondin type 1 motif, 2 NM 004567 1 PFKFB4 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 3p21-p22 4.90 4.97 NM 000854 1 GSTT2 glutathione S-transferase theta 2 22q11.23 3.23 3.28 NM 000300 1 PLA2G2A phospholipase A2, group IIA (platelets, synovial fluid) 1p35 3.01 3.05 NM0001201 EPHX1 epoxide hydrolase 1, microsomal (xenobiotic) 1q42.1 2.22 2.25 NM0026291 PGAM1 phosphoglycerate mutase 1 (brain) 10q25.3 2.13 2.16 NM0011901 BCAT2 branched chain aminotransferase 2, mitochondrial 19q13 1.61 1.63 NM 002905 1 RDH5 retinol dehydrogenase 5 (11-cis and 9-cis) 12q13-q14 1.62 1.64 NM0122601 HPCL2 2-hydroxyphytanoyl-CoA lyase 3p25.1 1.72 1.74 NM 005476 1 GNE UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase 9p11.2 1.87 1.90 NM0000391 APOA1 apolipoprotein A-I 11q23-q24 1.98 2.00 Ribosomal proteins NM 001020 1 RPS16 ribosomal protein S16 19q13.1 1.56 1.59 NM 052969 1 RPL39L ribosomal protein L39-like 3q27 2.30 2.34 DNA replication / repair NM 002553 1 ORC5L origin recognition complex, subunit 5-like (yeast) 7q22.1 1.67 1.69 NM_001983_1 ERCC1 excision repair cross-complementing rodent repair deficiency, 19q13.2-q13.3 1.82 1.84 complementation group 1 Hormone / Growth factor NM 007179 1 INSL6 insulin-like 6 9p24 1.66 1.68 NM0054481 BMP15 bone morphogenetic protein 15 Xp11.2 1.50 1.52 Unknown function NM0223331 TIAL1 TIA1 cytotoxic granule-associated RNA binding protein-like 1 10q 2.34 2.37 NM 014841 1 SNAP91 synaptosomal-associated protein, 91 kD homolog (mouse) 6q15 3.38 3.43 NM 025136 1 OPA3 optic atrophy 3 (autosomal recessive, with chorea and spastic 19q13.32 2.46 2.49 NM 012332 1 MT-ACT48 Mitochondrial Acyl-CoA Thioesterase Xp22.13 1.59 1.61 NM 013344 1 LZLP leucine zipper-like protein 11q13.1 1.58 1.61 NM 000607 1 ORM1 orosomucoid 1 9q31-q32 1.58 1.60 NM 006455 1 SC65 nucleolar autoantigen (55kD) similar to rat synaptonemal complex 17q21.1 1.56 1.58 NM0184751 TPARL TPA regulated locus 4q12 1.56 1.58 NM_021622_1 PLEKHA1 pleckstrin homology domain-containing, family A (phosphoinositide 10q26.3 1.54 1.56 binding specific) member 1 NM 006269 1 RP1 retinitis pigmentosa 1 (autosomal dominant) 8q11-q13 1.54 1.56 NM 014419 1 DKKL1 soggy-1 gene 19q13.33 1.53 1.56 NM 023036 1 DNAI2 dynein, axonemal, intermediate polypeptide 2 17q25 1.52 1.54 NM 001549 1 IFIT4 interferon-induced protein with tetratricopeptide repeats 4 10q24 1.52 1.54 NM 024614 1 FLJ13197 hypothetical protein FLJ13197 4p14 2.95 2.99 NM 023928 1 FLJ12389 hypothetical protein FLJ12389 similar to acetoacetyl-CoA synthetase 12q24.31 2.16 2.19 NM 018671 1 IRO039700 hypothetical protein IRO039700 15q26.1 2.12 2.15 NM 014674 1 KIAA0212 KIAA0212 gene product 3p26.1 2.01 2.04 NM 024706 1 FLJ13479 hypothetical protein FLJ13479 16p11.1 1.92 1.94 BC002509 1 MGC2941 hypothetical protein MGC2941 17p13.2 1.90 1.93 NM 018618 1 PRO2121 hypothetical protein PRO2121 1p36.33 1.89 1.91 NM 024668 1 FLJ20288 hypothetical protein FLJ20288 5q31.3 1.81 1.83 NM 025260 1 C6orf25 chromosome 6 open reading frame 25 6p21.31 1.74 1.76 NM 016068 1 LOC51024 CGI-135 protein 7q11.22 1.67 1.69 NM 024843 1 FLJ23462 duodenal cytochrome b 2q31.1 1.64 1.67 NM0175661 DKFZp434G05 hypothetical protein DKFZp434G0522 16q24.3 1.56 1.58 NM 032638 1 MGC2306 hypothetical protein MGC2306 3q22.1 1.55 1.58 NM 014746 1 KIAA0161 KIAA0161 gene product 2p25.3 1.54 1.56 NM0175661 DKFZp434G05 hypothetical protein DKFZp434G0522 16q24.3 1.56 1.58 NM 032638 1 MGC2306 hypothetical protein MGC2306 3q22.1 1.55 1.58 NM 014746 1 KIAA0161 KIAA0161 gene product 2p25.3 1.54 1.56 NM 018198 1 FLJ10737 hypothetical protein FLJ10737 1p36.23 1.51 1.54 NM 017877 1 FLJ20555 hypothetical protein FLJ20555 2p23.3 1.51 1.53 NM 018540 1 PRO2831 hypothetical protein PRO2831 6p21.1 1.51 1.53 Supplementary Figure 1 Empty NR1I2 VP-NR1I2 IMR32 SMS-KAN Misawa et al.